I am trying to assemble a pseudo-chromosome from a few thousand 130bp oligos with 30bp of overlap. I've aligned all of my reads to their reference and I have at least 20X coverage for each oligo. I've tried megahit and spades but I am not quite getting the correct scaffold. Is there an assembler that is more adept at this style of assembly?
If not, is there a tool that can generate consensus reads from NGS data?